public abstract class Atom extends ExperimentObject implements Serializable
Modifier and Type | Field and Description |
---|---|
static Atom |
C
The carbon atom.
|
static Atom |
F
The Fluorine atom.
|
static Atom |
H
The hydrogen atom.
|
static Atom |
He
The helium atom.
|
static Atom |
I
The Iodine atom.
|
protected HashMap<Integer,Double> |
isotopeMap
Map of the isotope masses relative to the monoisotopic peak (+1 for
carbon 13).
|
protected String |
letter
The single letter code of the atom.
|
static Atom |
Li
The phosphorus atom.
|
protected Double |
monoisotopicMass
The monoisotopic mass.
|
static Atom |
N
The nitrogen atom.
|
static Atom |
Na
The sodium atom.
|
protected String |
name
The name of the atom.
|
static Atom |
O
The oxygen atom.
|
static Atom |
P
The phosphorus atom.
|
protected HashMap<Integer,Double> |
representativeComposition
Map of the isotope representative composition of the stable isotopes.
|
static Atom |
S
The sulfur atom.
|
static Atom |
Se
The selenium atom.
|
Constructor and Description |
---|
Atom() |
Modifier and Type | Method and Description |
---|---|
static Atom |
getAtom(String shortName)
Returns the atom corresponding to the given short name.
|
Double |
getDifferenceToMonoisotopic(int isotopeNumber)
Returns the mass difference between the given isotope and the
monoisotopic mass.
|
static String[] |
getImplementedAtoms(boolean includeSelect)
Returns an array of implemented atoms indicated by their short name.
|
ArrayList<Integer> |
getImplementedIsotopes()
returns an unsorted list of isotopes for which a mass is available relative to the
monoisotopic peak (+1 for carbon 13).
|
Double |
getIsotopeMass(int isotopeNumber)
Returns the mass corresponding to the given isotope number.
|
String |
getLetter()
Returns the single letter code of the atom.
|
Double |
getMonoisotopicMass()
Returns the monoisotopic mass.
|
String |
getName()
Returns the name of the atom.
|
String |
toString() |
addUrParam, asLong, clearParametersMap, getUrParam, getUrParams, removeUrParam, setUrParams
getFirstLevel, getId, setFirstLevel, setId
jdoZooEvict, jdoZooGetBackup, jdoZooGetClassDef, jdoZooGetContext, jdoZooGetNode, jdoZooGetOid, jdoZooGetTimestamp, jdoZooHasState, jdoZooInit, jdoZooIsDeleted, jdoZooIsDetached, jdoZooIsDirty, jdoZooIsNew, jdoZooIsPersistent, jdoZooIsStateHollow, jdoZooIsTransactional, jdoZooMarkClean, jdoZooMarkDeleted, jdoZooMarkDetached, jdoZooMarkDirty, jdoZooMarkHollow, jdoZooMarkTransient, jdoZooSetOid, jdoZooSetTimestamp, zooActivateRead, zooActivateWrite, zooActivateWrite
public static final Atom H
public static final Atom N
public static final Atom O
public static final Atom C
public static final Atom S
public static final Atom P
public static final Atom He
public static final Atom Li
public static final Atom Na
public static final Atom Se
public static final Atom I
public static final Atom F
protected Double monoisotopicMass
protected HashMap<Integer,Double> isotopeMap
protected HashMap<Integer,Double> representativeComposition
protected String name
protected String letter
public static String[] getImplementedAtoms(boolean includeSelect)
includeSelect
- if true, the first item is set to '- Select -'public static Atom getAtom(String shortName)
shortName
- the short name of the atompublic Double getMonoisotopicMass()
public String getName()
public String getLetter()
public ArrayList<Integer> getImplementedIsotopes()
public Double getIsotopeMass(int isotopeNumber)
isotopeNumber
- the isotope number of interest relative to the
monoisotopic peak (+1 for carbon 13).public Double getDifferenceToMonoisotopic(int isotopeNumber)
isotopeNumber
- the isotope number relative to the monoisotopic peak
(+1 for carbon 13)public String toString()
toString
in class org.zoodb.api.impl.ZooPC
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